Colouration evo-devo: the developmental basis of intra-specific variation in cichlid pigmentation

Understanding why and how organisms diversify is a major goal of evolutionary biology. The fields of evolutionary developmental biology, evolutionary ecology, and population genetics have taken complementary approaches to this task, yet a lack of integration between these fields limits our understanding of the evolution of phenotypic diversity. Classical evo-devo tends to comprise comparative developmental biology between phylogenetically distant model organisms, while population genetics and evolutionary ecology studies often consider development as a ‘black-box’ between genotype and phenotype. Consequently, the role of development in the diversification of adaptive traits is not well understood. In this PhD thesis, I present a study of the development a trait exhibiting adaptive variation. Cichlid egg-spots are a well-suited model for investigating the development of diversifying traits. Evolving under sexual selection, egg-spots are dense aggregations of xanthophores and iridophores on haplochromine cichlid anal fins, exhibiting remarkable inter- and intra-specific variation. In a population of the generalist species Astatotilapia calliptera from the Lake Malawi/Nyasa radiation, variation in egg-spots maintains signal visibility across different depths. A Genome Wide Association Study (GWAS) identified oca2, a gene required for pigment synthesis in melanophores, as a candidate associated with egg-spot number variation. I present a study of A. calliptera egg-spot development and the developmental basis of intra-specific variation in egg-spot number. First, I characterise the development of egg-spots in embryo and juvenile stages in wild-type A. calliptera ‘kisiba/masoko’, describing a key role for iridophores initiating aggregations. I find consistent early development between littoral and benthic ecotypes, and identify developmental sources of variation between individuals, including developmental plasticity. Further, my results suggest differences in patterning rules from zebrafish stripe development, indicating evolutionary lability in pigment cell interactions. To examine the developmental role of candidate genes for egg-spot variation, I review the application of CRISPR/Cas9 technology to cichlid fish, defining the state-of-the-art of cichlid genome editing and synthesising resources. Next I establish CRISPR/Cas9 editing in A. calliptera: I report efficient editing and germline transmission of mutations, and demonstrate the null mutant phenotypes of biallelic oca2 mutants, with amelanistic embryos and adults. Finally, I examine the role of oca2 in the development of egg-spots. Comparing amelanistic and melanistic siblings, I find a higher number of egg-spots in oca2 null mutants. My comparison of juvenile development reveals delayed initial aggregations in oca2 null mutants followed by an increased number of iridophore clusters, indicating an effect on timing and an increased tendency to initiate new aggregations in amelanistic fins. Though growth patterns and egg-spot sizes do not differ, I find aggregations in amelanistic fins are more likely to occupy the proximal, faster-growing region of the fin. My findings not only validate the GWAS results, but also provide insights into the complexity of developmental divergence that underlies phenotypic divergence. The results I present in this thesis provide a developmental connection between the genotypic, phenotypic, and environmental divergence in A. calliptera egg-spots. In particular, my work demonstrates the variety of mechanisms by which developmental processes transmit and integrate variation from both genetic and environmental sources, therefore contributing to our understanding of the interplay between these factors and highlighting the importance of studying development in micro- and eco-evolutionary contexts.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2025

Author dc:creator

• Clark, Bethan

Advisor dc:contributor.advisor

• Santos, Emília

• developmental biology
• cichlid fish
• evolutionary biology
• development
• evolution
• cichlid
• pigmentation
• variation
• evo-devo
• eco-evo-devo
• micro-evo-devo

Licence

• https://www.repository.cam.ac.uk/bitstreams/6f96200e-f831-4e3f-82d9-979db4db2bd8/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

Author Identifier

0000-0001-8968-0572

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/395375